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(1) 16 - initial time reserve
(2) 8 - time added each turn for moving around the map
(3) 1 - time for a battle (if the battle ends sooner, the time reserve doesn't accumulate)
The time reserve (1) is used for securing the game and for moving around the map (2) and battles (3), if a battle takes more than a minute.
It seems this was the case a few versions of the HD mod ago.
There are also persistent rumors that the chess timer is buggy and that work is constantly being done on it in the HD mod.
P.S. And also - 1 minute per battle with an initial time reserve of 16 is essentially a blitz game.